Starting phenix.real_space_refine on Tue Sep 24 08:20:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nll_12465/09_2024/7nll_12465.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nll_12465/09_2024/7nll_12465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nll_12465/09_2024/7nll_12465.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nll_12465/09_2024/7nll_12465.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nll_12465/09_2024/7nll_12465.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nll_12465/09_2024/7nll_12465.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.078 sd= 0.125 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2915 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 3220 2.51 5 N 829 2.21 5 O 985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5056 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1501 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 184} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1494 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 183} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1021 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "C" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1012 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'RTV': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'RTV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.32, per 1000 atoms: 0.66 Number of scatterers: 5056 At special positions: 0 Unit cell: (92.92, 57.57, 105.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 985 8.00 N 829 7.00 C 3220 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 621.6 milliseconds 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1184 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 10 sheets defined 15.2% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.597A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.330A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.330A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN B 409 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'D' and resid 337 through 343 removed outlier: 3.597A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 371 Processing helix chain 'D' and resid 383 through 388 removed outlier: 4.329A pdb=" N ASN D 388 " --> pdb=" O PRO D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 410 removed outlier: 4.329A pdb=" N ARG D 408 " --> pdb=" O GLY D 404 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN D 409 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 438 through 443 Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 114 through 118 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.614A pdb=" N TYR C 109 " --> pdb=" O CYS B 379 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AA5, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AA7, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'A' and resid 11 through 12 removed outlier: 6.753A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.753A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) 171 hydrogen bonds defined for protein. 417 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.39 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1620 1.34 - 1.46: 1413 1.46 - 1.58: 2139 1.58 - 1.70: 0 1.70 - 1.81: 24 Bond restraints: 5196 Sorted by residual: bond pdb=" C5 RTV D1001 " pdb=" O5 RTV D1001 " ideal model delta sigma weight residual 1.411 1.436 -0.025 2.00e-02 2.50e+03 1.52e+00 bond pdb=" C5 RTV B1001 " pdb=" O5 RTV B1001 " ideal model delta sigma weight residual 1.411 1.435 -0.024 2.00e-02 2.50e+03 1.49e+00 bond pdb=" C1 RTV B1001 " pdb=" O5 RTV B1001 " ideal model delta sigma weight residual 1.406 1.428 -0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" C2 RTV B1001 " pdb=" C3 RTV B1001 " ideal model delta sigma weight residual 1.547 1.525 0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" C4 RTV B1001 " pdb=" C5 RTV B1001 " ideal model delta sigma weight residual 1.547 1.526 0.021 2.00e-02 2.50e+03 1.12e+00 ... (remaining 5191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.88: 6519 0.88 - 1.77: 434 1.77 - 2.65: 85 2.65 - 3.53: 36 3.53 - 4.42: 8 Bond angle restraints: 7082 Sorted by residual: angle pdb=" N TYR C 109 " pdb=" CA TYR C 109 " pdb=" C TYR C 109 " ideal model delta sigma weight residual 108.34 105.46 2.88 1.64e+00 3.72e-01 3.09e+00 angle pdb=" N TYR A 109 " pdb=" CA TYR A 109 " pdb=" C TYR A 109 " ideal model delta sigma weight residual 108.34 105.46 2.88 1.64e+00 3.72e-01 3.08e+00 angle pdb=" CA TYR B 369 " pdb=" CB TYR B 369 " pdb=" CG TYR B 369 " ideal model delta sigma weight residual 113.90 116.98 -3.08 1.80e+00 3.09e-01 2.93e+00 angle pdb=" CA TYR D 369 " pdb=" CB TYR D 369 " pdb=" CG TYR D 369 " ideal model delta sigma weight residual 113.90 116.95 -3.05 1.80e+00 3.09e-01 2.87e+00 angle pdb=" N ASP A 119 " pdb=" CA ASP A 119 " pdb=" C ASP A 119 " ideal model delta sigma weight residual 111.36 113.10 -1.74 1.09e+00 8.42e-01 2.54e+00 ... (remaining 7077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.37: 2892 22.37 - 44.73: 96 44.73 - 67.10: 14 67.10 - 89.47: 12 89.47 - 111.84: 14 Dihedral angle restraints: 3028 sinusoidal: 1140 harmonic: 1888 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 96 " pdb=" CB CYS C 96 " ideal model delta sinusoidal sigma weight residual 93.00 57.00 36.00 1 1.00e+01 1.00e-02 1.83e+01 dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 96 " pdb=" CB CYS A 96 " ideal model delta sinusoidal sigma weight residual 93.00 57.02 35.98 1 1.00e+01 1.00e-02 1.83e+01 dihedral pdb=" C2 RTV D1001 " pdb=" C3 RTV D1001 " pdb=" C4 RTV D1001 " pdb=" C5 RTV D1001 " ideal model delta sinusoidal sigma weight residual -57.83 54.01 -111.84 1 3.00e+01 1.11e-03 1.46e+01 ... (remaining 3025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.000: 745 1.000 - 2.000: 0 2.000 - 3.001: 0 3.001 - 4.001: 0 4.001 - 5.001: 2 Chirality restraints: 747 Sorted by residual: chirality pdb=" C2 RTV D1001 " pdb=" C1 RTV D1001 " pdb=" C3 RTV D1001 " pdb=" N2 RTV D1001 " both_signs ideal model delta sigma weight residual False 2.50 -2.50 5.00 2.00e-01 2.50e+01 6.25e+02 chirality pdb=" C2 RTV B1001 " pdb=" C1 RTV B1001 " pdb=" C3 RTV B1001 " pdb=" N2 RTV B1001 " both_signs ideal model delta sigma weight residual False 2.50 -2.50 5.00 2.00e-01 2.50e+01 6.25e+02 chirality pdb=" CA ILE A 51 " pdb=" N ILE A 51 " pdb=" C ILE A 51 " pdb=" CB ILE A 51 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 744 not shown) Planarity restraints: 927 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 116 " 0.010 2.00e-02 2.50e+03 7.11e-03 1.27e+00 pdb=" CG TRP C 116 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP C 116 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP C 116 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 116 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 116 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 116 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 116 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 116 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 116 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 116 " -0.010 2.00e-02 2.50e+03 6.98e-03 1.22e+00 pdb=" CG TRP A 116 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP A 116 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 116 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 116 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 116 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 116 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 116 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 116 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 116 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 109 " -0.006 2.00e-02 2.50e+03 6.69e-03 8.94e-01 pdb=" CG TYR C 109 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR C 109 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 109 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 109 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 109 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 109 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 109 " 0.001 2.00e-02 2.50e+03 ... (remaining 924 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1059 2.78 - 3.31: 4439 3.31 - 3.84: 8558 3.84 - 4.37: 10483 4.37 - 4.90: 17832 Nonbonded interactions: 42371 Sorted by model distance: nonbonded pdb=" ND2 ASN B 343 " pdb=" O7 RTV B1001 " model vdw 2.255 3.120 nonbonded pdb=" N GLY C 15 " pdb=" O LEU C 86 " model vdw 2.557 3.120 nonbonded pdb=" N GLY A 15 " pdb=" O LEU A 86 " model vdw 2.557 3.120 nonbonded pdb=" N GLN C 13 " pdb=" OE1 GLN C 13 " model vdw 2.571 3.120 nonbonded pdb=" N GLN A 13 " pdb=" OE1 GLN A 13 " model vdw 2.572 3.120 ... (remaining 42366 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 133) selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 333 through 381 or (resid 382 and (name N or name CA or na \ me C or name O or name CB )) or resid 383 through 527 or resid 1001)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.540 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5196 Z= 0.176 Angle : 0.549 4.419 7082 Z= 0.304 Chirality : 0.263 5.001 747 Planarity : 0.004 0.023 927 Dihedral : 15.471 111.836 1814 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.31), residues: 648 helix: -0.59 (0.84), residues: 36 sheet: 2.74 (0.37), residues: 164 loop : 0.35 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 116 HIS 0.000 0.000 HIS B 519 PHE 0.012 0.001 PHE B 347 TYR 0.016 0.001 TYR C 109 ARG 0.002 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8321 (m-30) cc_final: 0.8049 (m-30) REVERT: B 483 VAL cc_start: 0.8283 (t) cc_final: 0.8058 (m) REVERT: D 493 GLN cc_start: 0.8064 (tp40) cc_final: 0.7738 (tp40) REVERT: A 73 ASP cc_start: 0.8075 (t0) cc_final: 0.7862 (t0) REVERT: C 32 TYR cc_start: 0.9068 (m-80) cc_final: 0.8781 (m-80) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.9438 time to fit residues: 161.1805 Evaluate side-chains 116 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 20.0000 chunk 25 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 58 optimal weight: 20.0000 overall best weight: 10.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 ASN A 74 ASN C 39 GLN C 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 5196 Z= 0.424 Angle : 0.652 7.606 7082 Z= 0.348 Chirality : 0.050 0.302 747 Planarity : 0.005 0.035 927 Dihedral : 6.811 43.896 770 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 4.21 % Allowed : 12.84 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.31), residues: 648 helix: -0.94 (0.79), residues: 37 sheet: 1.30 (0.37), residues: 201 loop : 0.07 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 116 HIS 0.001 0.001 HIS B 519 PHE 0.017 0.002 PHE D 347 TYR 0.022 0.002 TYR B 495 ARG 0.004 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8419 (m-30) cc_final: 0.8110 (m-30) REVERT: D 420 ASP cc_start: 0.8513 (m-30) cc_final: 0.8135 (m-30) REVERT: D 493 GLN cc_start: 0.7984 (tp40) cc_final: 0.7729 (tp40) REVERT: D 498 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8170 (mp10) REVERT: A 6 GLU cc_start: 0.7959 (mp0) cc_final: 0.7621 (mp0) REVERT: A 31 ASP cc_start: 0.8020 (t0) cc_final: 0.7741 (t0) REVERT: A 46 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7701 (pt0) REVERT: A 108 THR cc_start: 0.9303 (m) cc_final: 0.9016 (p) REVERT: A 128 THR cc_start: 0.8775 (m) cc_final: 0.8572 (p) REVERT: C 32 TYR cc_start: 0.9201 (m-80) cc_final: 0.8904 (m-80) REVERT: C 84 ASN cc_start: 0.8751 (m110) cc_final: 0.8548 (m-40) REVERT: C 90 ASP cc_start: 0.8059 (m-30) cc_final: 0.7839 (m-30) REVERT: C 95 TYR cc_start: 0.9167 (m-80) cc_final: 0.8680 (m-80) outliers start: 22 outliers final: 5 residues processed: 136 average time/residue: 0.7849 time to fit residues: 113.0768 Evaluate side-chains 118 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 111 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 40.0000 chunk 18 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN B 501 ASN D 409 GLN A 74 ASN A 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5196 Z= 0.212 Angle : 0.545 8.297 7082 Z= 0.288 Chirality : 0.043 0.152 747 Planarity : 0.004 0.035 927 Dihedral : 5.651 41.680 770 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.26 % Allowed : 18.20 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.31), residues: 648 helix: -1.09 (0.77), residues: 37 sheet: 1.40 (0.36), residues: 187 loop : -0.18 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 116 HIS 0.000 0.000 HIS B 519 PHE 0.007 0.001 PHE A 68 TYR 0.017 0.001 TYR B 369 ARG 0.008 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: B 418 ILE cc_start: 0.8350 (mp) cc_final: 0.8090 (mm) REVERT: B 420 ASP cc_start: 0.8403 (m-30) cc_final: 0.8173 (m-30) REVERT: B 493 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7304 (tm-30) REVERT: D 420 ASP cc_start: 0.8535 (m-30) cc_final: 0.8198 (m-30) REVERT: D 493 GLN cc_start: 0.8021 (tp40) cc_final: 0.7765 (tp40) REVERT: D 498 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8105 (mp10) REVERT: A 6 GLU cc_start: 0.8037 (mp0) cc_final: 0.7531 (mp0) REVERT: A 31 ASP cc_start: 0.8065 (t0) cc_final: 0.7839 (t0) REVERT: A 46 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7802 (pt0) REVERT: A 103 SER cc_start: 0.8613 (m) cc_final: 0.8396 (p) REVERT: C 32 TYR cc_start: 0.9170 (m-80) cc_final: 0.8907 (m-80) REVERT: C 84 ASN cc_start: 0.8737 (m110) cc_final: 0.8517 (m-40) REVERT: C 90 ASP cc_start: 0.8094 (m-30) cc_final: 0.7871 (m-30) REVERT: C 95 TYR cc_start: 0.9146 (m-80) cc_final: 0.8732 (m-80) outliers start: 17 outliers final: 8 residues processed: 129 average time/residue: 0.7957 time to fit residues: 108.7730 Evaluate side-chains 122 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 30 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 39 optimal weight: 0.4980 chunk 58 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 51 optimal weight: 30.0000 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN D 409 GLN A 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5196 Z= 0.192 Angle : 0.526 9.227 7082 Z= 0.276 Chirality : 0.043 0.151 747 Planarity : 0.004 0.033 927 Dihedral : 5.328 41.235 770 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.60 % Allowed : 17.82 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.31), residues: 648 helix: -1.16 (0.77), residues: 37 sheet: 1.21 (0.37), residues: 187 loop : -0.23 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 116 HIS 0.000 0.000 HIS B 519 PHE 0.007 0.001 PHE A 68 TYR 0.017 0.001 TYR B 369 ARG 0.005 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 113 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 493 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7298 (tm-30) REVERT: D 420 ASP cc_start: 0.8519 (m-30) cc_final: 0.8175 (m-30) REVERT: D 493 GLN cc_start: 0.8020 (tp40) cc_final: 0.7804 (tp40) REVERT: D 498 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8100 (mp10) REVERT: A 6 GLU cc_start: 0.8113 (mp0) cc_final: 0.7654 (mp0) REVERT: A 31 ASP cc_start: 0.8076 (t0) cc_final: 0.7867 (t0) REVERT: A 46 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7860 (pt0) REVERT: A 103 SER cc_start: 0.8619 (m) cc_final: 0.8400 (p) REVERT: C 32 TYR cc_start: 0.9169 (m-80) cc_final: 0.8884 (m-80) REVERT: C 84 ASN cc_start: 0.8732 (m110) cc_final: 0.8506 (m-40) REVERT: C 90 ASP cc_start: 0.8119 (m-30) cc_final: 0.7858 (m-30) REVERT: C 95 TYR cc_start: 0.9139 (m-80) cc_final: 0.8692 (m-80) outliers start: 24 outliers final: 14 residues processed: 128 average time/residue: 0.7850 time to fit residues: 106.6725 Evaluate side-chains 126 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 42 optimal weight: 0.0020 chunk 31 optimal weight: 30.0000 chunk 55 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 overall best weight: 4.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5196 Z= 0.227 Angle : 0.537 9.654 7082 Z= 0.283 Chirality : 0.043 0.151 747 Planarity : 0.004 0.031 927 Dihedral : 5.321 40.813 770 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 5.56 % Allowed : 18.39 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.31), residues: 648 helix: -0.51 (0.94), residues: 31 sheet: 1.06 (0.36), residues: 187 loop : -0.31 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 436 HIS 0.001 0.000 HIS B 519 PHE 0.019 0.001 PHE D 486 TYR 0.016 0.001 TYR B 369 ARG 0.004 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 114 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: B 493 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7299 (tm-30) REVERT: B 498 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8354 (mp10) REVERT: D 420 ASP cc_start: 0.8531 (m-30) cc_final: 0.8194 (m-30) REVERT: D 493 GLN cc_start: 0.8022 (tp40) cc_final: 0.7759 (tp40) REVERT: D 498 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8143 (mp10) REVERT: A 6 GLU cc_start: 0.8299 (mp0) cc_final: 0.7907 (mp0) REVERT: A 46 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7934 (pt0) REVERT: A 103 SER cc_start: 0.8688 (m) cc_final: 0.8466 (p) REVERT: C 32 TYR cc_start: 0.9202 (m-80) cc_final: 0.8986 (m-80) REVERT: C 84 ASN cc_start: 0.8757 (m110) cc_final: 0.8534 (m-40) REVERT: C 90 ASP cc_start: 0.8182 (m-30) cc_final: 0.7917 (m-30) REVERT: C 95 TYR cc_start: 0.9151 (m-80) cc_final: 0.8752 (m-80) outliers start: 29 outliers final: 21 residues processed: 130 average time/residue: 0.7627 time to fit residues: 105.2272 Evaluate side-chains 137 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 112 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 51 optimal weight: 30.0000 chunk 28 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 20 optimal weight: 0.3980 chunk 32 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5196 Z= 0.179 Angle : 0.524 11.775 7082 Z= 0.272 Chirality : 0.042 0.142 747 Planarity : 0.004 0.032 927 Dihedral : 5.055 41.169 770 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 5.56 % Allowed : 19.92 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.31), residues: 648 helix: -0.26 (0.97), residues: 30 sheet: 1.20 (0.36), residues: 177 loop : -0.34 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 436 HIS 0.000 0.000 HIS D 519 PHE 0.007 0.001 PHE D 486 TYR 0.016 0.001 TYR B 369 ARG 0.004 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: B 493 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7272 (tm-30) REVERT: B 498 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8462 (mp10) REVERT: D 420 ASP cc_start: 0.8501 (m-30) cc_final: 0.8159 (m-30) REVERT: D 493 GLN cc_start: 0.8020 (tp40) cc_final: 0.7771 (tp40) REVERT: D 498 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8104 (mp10) REVERT: A 6 GLU cc_start: 0.8292 (mp0) cc_final: 0.7767 (mp0) REVERT: A 45 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7625 (mtt180) REVERT: A 76 LYS cc_start: 0.8219 (mtmm) cc_final: 0.7908 (ptpp) REVERT: C 32 TYR cc_start: 0.9184 (m-80) cc_final: 0.8940 (m-80) REVERT: C 84 ASN cc_start: 0.8722 (m110) cc_final: 0.8515 (m-40) REVERT: C 90 ASP cc_start: 0.8173 (m-30) cc_final: 0.7929 (m-30) REVERT: C 95 TYR cc_start: 0.9152 (m-80) cc_final: 0.8784 (m-80) outliers start: 29 outliers final: 19 residues processed: 136 average time/residue: 0.8147 time to fit residues: 117.0480 Evaluate side-chains 129 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 52 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 38 optimal weight: 30.0000 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 5196 Z= 0.250 Angle : 0.559 12.074 7082 Z= 0.290 Chirality : 0.044 0.150 747 Planarity : 0.004 0.033 927 Dihedral : 5.256 40.203 770 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 5.75 % Allowed : 21.65 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.31), residues: 648 helix: -0.28 (0.98), residues: 30 sheet: 0.88 (0.36), residues: 187 loop : -0.36 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 436 HIS 0.001 0.000 HIS B 519 PHE 0.008 0.001 PHE A 68 TYR 0.015 0.001 TYR B 369 ARG 0.003 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 111 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: B 457 ARG cc_start: 0.9057 (ttt90) cc_final: 0.8846 (ttt90) REVERT: B 493 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7243 (tm-30) REVERT: B 498 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8463 (mp10) REVERT: D 409 GLN cc_start: 0.8680 (tt0) cc_final: 0.8330 (tt0) REVERT: D 420 ASP cc_start: 0.8483 (m-30) cc_final: 0.8162 (m-30) REVERT: D 493 GLN cc_start: 0.8011 (tp40) cc_final: 0.7780 (tp40) REVERT: D 498 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8163 (mp10) REVERT: D 517 LEU cc_start: 0.8135 (tp) cc_final: 0.7908 (tt) REVERT: A 6 GLU cc_start: 0.7723 (mp0) cc_final: 0.7353 (mp0) REVERT: A 45 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7612 (mtt180) REVERT: A 73 ASP cc_start: 0.7994 (t0) cc_final: 0.7711 (t0) REVERT: C 32 TYR cc_start: 0.9208 (m-80) cc_final: 0.8962 (m-80) REVERT: C 90 ASP cc_start: 0.8229 (m-30) cc_final: 0.7958 (m-30) REVERT: C 95 TYR cc_start: 0.9149 (m-80) cc_final: 0.8719 (m-80) REVERT: C 125 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8809 (t) outliers start: 30 outliers final: 20 residues processed: 129 average time/residue: 0.7794 time to fit residues: 106.4685 Evaluate side-chains 133 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 0.0670 chunk 11 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 30 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 53 optimal weight: 30.0000 chunk 57 optimal weight: 5.9990 overall best weight: 4.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5196 Z= 0.218 Angle : 0.583 16.225 7082 Z= 0.292 Chirality : 0.043 0.144 747 Planarity : 0.004 0.035 927 Dihedral : 5.140 40.510 770 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.60 % Allowed : 22.99 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.31), residues: 648 helix: -0.39 (0.98), residues: 30 sheet: 1.01 (0.37), residues: 177 loop : -0.40 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 436 HIS 0.001 0.000 HIS B 519 PHE 0.007 0.001 PHE A 68 TYR 0.016 0.001 TYR B 369 ARG 0.002 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 1.346 Fit side-chains revert: symmetry clash REVERT: B 408 ARG cc_start: 0.8930 (tmm160) cc_final: 0.8498 (ppt170) REVERT: B 457 ARG cc_start: 0.9060 (ttt90) cc_final: 0.8825 (ttt90) REVERT: B 493 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.7228 (tm-30) REVERT: B 498 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8384 (mp10) REVERT: D 409 GLN cc_start: 0.8669 (tt0) cc_final: 0.8343 (tt0) REVERT: D 420 ASP cc_start: 0.8453 (m-30) cc_final: 0.8124 (m-30) REVERT: D 493 GLN cc_start: 0.8027 (tp40) cc_final: 0.7800 (tp40) REVERT: D 498 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8138 (mp10) REVERT: D 517 LEU cc_start: 0.8136 (tp) cc_final: 0.7915 (tt) REVERT: A 6 GLU cc_start: 0.7725 (mp0) cc_final: 0.7380 (mp0) REVERT: A 31 ASP cc_start: 0.8095 (t0) cc_final: 0.7758 (t0) REVERT: A 45 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7619 (mtt180) REVERT: C 32 TYR cc_start: 0.9212 (m-80) cc_final: 0.8975 (m-80) REVERT: C 90 ASP cc_start: 0.8230 (m-30) cc_final: 0.7958 (m-30) REVERT: C 95 TYR cc_start: 0.9158 (m-80) cc_final: 0.8734 (m-80) outliers start: 24 outliers final: 19 residues processed: 125 average time/residue: 0.7747 time to fit residues: 103.0226 Evaluate side-chains 129 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5196 Z= 0.280 Angle : 0.588 12.671 7082 Z= 0.303 Chirality : 0.044 0.154 747 Planarity : 0.004 0.034 927 Dihedral : 5.355 39.528 770 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.79 % Allowed : 23.18 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.31), residues: 648 helix: -0.49 (0.98), residues: 30 sheet: 0.71 (0.36), residues: 187 loop : -0.44 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 436 HIS 0.001 0.001 HIS B 519 PHE 0.009 0.001 PHE A 68 TYR 0.015 0.001 TYR B 369 ARG 0.003 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: B 457 ARG cc_start: 0.9063 (ttt90) cc_final: 0.8808 (ttt90) REVERT: B 493 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: B 498 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8452 (mp10) REVERT: D 420 ASP cc_start: 0.8472 (m-30) cc_final: 0.8221 (m-30) REVERT: D 493 GLN cc_start: 0.8015 (tp40) cc_final: 0.7788 (tp40) REVERT: D 498 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8163 (mp10) REVERT: D 517 LEU cc_start: 0.8160 (tp) cc_final: 0.7946 (tt) REVERT: A 6 GLU cc_start: 0.7777 (mp0) cc_final: 0.7412 (mp0) REVERT: A 31 ASP cc_start: 0.8008 (t0) cc_final: 0.7610 (t0) REVERT: A 45 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7610 (mtt180) REVERT: C 32 TYR cc_start: 0.9227 (m-80) cc_final: 0.9004 (m-80) REVERT: C 46 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7802 (pt0) REVERT: C 82 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.7384 (tm-30) REVERT: C 90 ASP cc_start: 0.8238 (m-30) cc_final: 0.7958 (m-30) outliers start: 25 outliers final: 20 residues processed: 124 average time/residue: 0.7359 time to fit residues: 97.1241 Evaluate side-chains 129 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 103 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 chunk 15 optimal weight: 0.0970 chunk 46 optimal weight: 6.9990 overall best weight: 3.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5196 Z= 0.180 Angle : 0.547 10.439 7082 Z= 0.284 Chirality : 0.043 0.141 747 Planarity : 0.004 0.034 927 Dihedral : 5.043 40.971 770 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.79 % Allowed : 23.18 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.31), residues: 648 helix: -0.60 (0.98), residues: 30 sheet: 0.90 (0.37), residues: 177 loop : -0.46 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 436 HIS 0.000 0.000 HIS B 519 PHE 0.005 0.001 PHE B 490 TYR 0.016 0.001 TYR B 369 ARG 0.002 0.000 ARG B 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: B 408 ARG cc_start: 0.8853 (tmm160) cc_final: 0.8476 (ppt170) REVERT: B 493 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7211 (tm-30) REVERT: B 498 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8365 (mp10) REVERT: D 409 GLN cc_start: 0.8679 (tt0) cc_final: 0.8458 (tt0) REVERT: D 420 ASP cc_start: 0.8426 (m-30) cc_final: 0.8096 (m-30) REVERT: D 493 GLN cc_start: 0.8016 (tp40) cc_final: 0.7796 (tp40) REVERT: D 498 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8102 (mp10) REVERT: D 517 LEU cc_start: 0.8120 (tp) cc_final: 0.7912 (tt) REVERT: A 6 GLU cc_start: 0.7627 (mp0) cc_final: 0.7274 (mp0) REVERT: A 31 ASP cc_start: 0.8001 (t0) cc_final: 0.7587 (t0) REVERT: A 45 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7560 (mtt180) REVERT: C 32 TYR cc_start: 0.9203 (m-80) cc_final: 0.8973 (m-80) REVERT: C 46 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7799 (pt0) REVERT: C 90 ASP cc_start: 0.8242 (m-30) cc_final: 0.7948 (m-30) REVERT: C 95 TYR cc_start: 0.9103 (m-80) cc_final: 0.8810 (m-80) outliers start: 25 outliers final: 20 residues processed: 124 average time/residue: 0.7395 time to fit residues: 97.5263 Evaluate side-chains 132 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 50 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.100123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.085091 restraints weight = 8600.940| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.71 r_work: 0.3053 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5196 Z= 0.167 Angle : 0.546 10.218 7082 Z= 0.283 Chirality : 0.043 0.135 747 Planarity : 0.004 0.033 927 Dihedral : 4.913 41.047 770 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.21 % Allowed : 23.95 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.31), residues: 648 helix: -0.61 (0.99), residues: 30 sheet: 1.11 (0.38), residues: 167 loop : -0.49 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 436 HIS 0.000 0.000 HIS B 519 PHE 0.004 0.001 PHE B 490 TYR 0.016 0.001 TYR B 369 ARG 0.002 0.000 ARG B 403 =============================================================================== Job complete usr+sys time: 2192.72 seconds wall clock time: 38 minutes 47.91 seconds (2327.91 seconds total)